1.軟件的安裝：

網站：http://www.megasoftware.net/

windows上安裝，下載windows-command line（cc）版本的，格式為zip，解壓之後，裏面有兩個主程序，MEGACC和MEGA-PROTO，安裝完後之後，將megacc的環境變量添加到系統的環境變量中（自行百度）

Linux安裝：根據自身系統的版本，選擇相應的Linux版本，我的是Ubuntu系統，因此選擇的Debian，下載最新版本

sudo dpkg -i megaccamd64.ded ##但是Linux版本的沒有mega-proto，所以還需要下載一個windows版本的megacc，借用其mega-proto生成所需要的mao文件（本人就傻的一直找Linux版本的mega-proto，發現沒有，坑了一下午。。。）

安裝完成即可使用，不需要環境變量的設置。

2.程序的運行：

個人習慣先查看軟件的使用幫助手冊

megacc -h ##會顯示megacc的具體參數意義及使用方法

3.用法舉例

megacc -a setting.mao -d inputfile.fasta(inputfile.meg) ##可以不指定輸出選項，

Usage: MEGA-CC.exe -a /pathTo/analysisFile.mao -d /pathTo/dataFile.meg [-t /pathTo/treeFile.nwk][OPTIONS]

   -a --analysisOptions 
       MEGA Analysis Options File     *required*
 
 由mega-proto軟件產生，具體使用見下載包中附帶的說明書 mao文件即參數設置文件
       Specify the full path to the Mega Analysis Options (.mao) file.  
       This file tells MEGA-CC which analysis to perform as well as
       which options to use

   -c --calibration 
       Calibration file *optional*
       Specify the full path to a calibration file that you wish to use. The calibration 
       file is used to provide calibration data for tree timing methods
 
.

   -d --data 
       Data File         *required*
       Specify the full  or relative path to the data file you wish to 
       analyze.  MEGA (.meg), and Fasta files are supported for 
       all analyses. For distance matrices the MEGA (.meg) format is required.

   -f --format *applies to sequence alignment only*
       Export format for sequence alignment
       Sequence alignments can be exported in either the native .meg
       or FASTA format.
       Format values:
         MEGA
         Fasta

   -g --groups 
       Groups file *optional*
       Specify the full path to the groups file that you wish to use. This file organizes 
       taxa into groups where each line in the file is a key value pair of the form 
             taxonName=groupName 
       Group information is used for certain analyses, for instance, specifying which taxon/taxa 
       comprise the outgroup for the timetree analysis 

   -h --help 
       Help
       Prints this help file document
   -n --noSummary: Do not write out the analysis summary file
       By default a file that gives an analysis summary is written.
       This option suppresses the export of that file. However, if
       any important messages are generated by the application, they
       will be written to this file regardless.

   -o --outfile     *optional*
       Output Path / Output Dir
       Specify the full path and base filename (e.g. /myResultsDirectory/myResultName) or
       simply the full path and directory of where to save the file
       (e.g. /myResultsDirectory) in which case, a unique filename will be chosen
       automatically for you.
   -pfc --partition-frequency-cutoff
       Partition Frequency Cutoff (a value between 0.0 and 1.0 - default is 0.5) *optional*
       When bootstrapping is used for tree construction a list of partitions and
       frequencies is written to a text file. The partition frequency cutoff
       causes any partitions whose frequency is less than the cutoff value
       to be ommited from this text file. Set this value to 0.0 to include
       all partitions.
   -r --recursive
       Recursive directory search *optional*
       If a directory is specified for analysis by default MEGA only searches
       the contents of that folder and not any of it‘s children.  To include the
       contents of all folders under the one specified, use this option.

   -s --silent: Do not write out the progress updates
       This option prevents progress updates from being written to stdout.

   -t --tree     *required for some analyses*
       Tree File
       Specify the full path to the tree file you wish to use. (Some 
       analyses requires a user provided tree, or allow you to provide 
       your own)

          If no output path is specified, results will be saved in the same directory
       as the input data file, with a unique name.

不懂就看看幫助文件。。。

4.megacc既可以分析單個的文件，也可以進行多文件處理

單文件處理方式：

megacc -a settings.mao -d inputfile.fasta

megacc -a settings.mao -d mut.txt

在mut.txt中包含要處理的文件的路徑，這樣megacc就會自己按序執行（可以看出，這些待處理的文件的參數設置是一樣的）

mut.txt的內容如下所示：
/home/lmt/Desktop/megacc/aa.meg
/home/lmt/Desktop/megacc/bb.meg   ##記得輸入絕對路徑，這樣可以保證不會出錯

megacc的進行多序列比對